Jax's MK3 skin depicts him with a clean-shaven face. But in the original MK3 game, he had a mustache.
Liu Kang's MK1 skin has him with a bandanna and armbands, in the original game he doesn't have a bandanna and armbands.
Sub-Zero was raised in China, but he does a Japanese Tea Ceremony. This was intentional as He was showing cultural courtesy to Scorpion who is Japanese as a form of respect. So it would make sense that Sub-Zero would perform a Japanese Tea Ceremony.
During Cassie Cage's Selfie fatality, she is seen holding her cellphone upright. However after taking a picture, the picture is in horizontal position.
It is well established in the "Alien" film series that the xenomorph's blood is acidic, and will eat through almost anything. Sub-Zero even claims in an intro that he will freeze the Alien's "acid blood." As such, many of the Fatalities performed on the creature should be damaging, if not fatal, to the performer; instead, he/she is unharmed by all that blood.
Takeda's name is pronounced in the Anglo-American fashion (Ti-key-da) when it should be pronounced as Ta-kay-da.
Kung Jin claims Raiden sent Kung Lao to fight Shao Khan, leading to his death. In actuality, Lao was sent to fight Shang Tsung, Quan Chi, and Kintaro, after which Khan snuck up behind him to kill him.